During processing and preservation, various physical changes (e.g., melting, crystallization, glass transition, and complex formation) occur in food products, which affect their quality. Thermal analysis is useful to understand the physical changes. This article focuses on the effect of starch melting and glass transition on the quality of cookie. Melting temperature of starch increased with decreasing water content of the cookie dough. When starch melting during baking was prevented by pre-dehydrated baking and/or stepwise baking, in vitro starch digestibility of cookie was reduced. This is because crystalline form is more resistant to enzymatic action than the amorphous form. Reduction of starch digestibility has attracted much attention in recent years with respect to potential beneficial effects on metabolic responses. Amorphous part of cookie products is commonly in a glass state, and glass to rubber transition occurs by water sorption. Then, brittle texture of cookie changes to a ductile one. Glass transition temperature of cookie was modified by the addition of low-molecular carbohydrates. This result suggests that sugar composition plays an important role in the texture properties of cookie samples.